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Mach N. The forecasting power of the mucin-microbiome interplay in livestock respiratory diseases. Vet Q 2024; 44:1-18. [PMID: 38606662 PMCID: PMC11018052 DOI: 10.1080/01652176.2024.2340003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 03/31/2024] [Indexed: 04/13/2024] Open
Abstract
Complex respiratory diseases are a significant challenge for the livestock industry worldwide. These diseases considerably impact animal health and welfare and cause severe economic losses. One of the first lines of pathogen defense combines the respiratory tract mucus, a highly viscous material primarily composed of mucins, and a thriving multi-kingdom microbial ecosystem. The microbiome-mucin interplay protects from unwanted substances and organisms, but its dysfunction may enable pathogenic infections and the onset of respiratory disease. Emerging evidence also shows that noncoding regulatory RNAs might modulate the structure and function of the microbiome-mucin relationship. This opinion paper unearths the current understanding of the triangular relationship between mucins, the microbiome, and noncoding RNAs in the context of respiratory infections in animals of veterinary interest. There is a need to look at these molecular underpinnings that dictate distinct health and disease outcomes to implement effective prevention, surveillance, and timely intervention strategies tailored to the different epidemiological contexts.
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Affiliation(s)
- Núria Mach
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
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2
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Marín-Miret J, Pérez-Cobas AE, Domínguez-Santos R, Pérez-Rocher B, Latorre A, Moya A. Adaptability of the gut microbiota of the German cockroach Blattella germanica to a periodic antibiotic treatment. Microbiol Res 2024; 287:127863. [PMID: 39106785 DOI: 10.1016/j.micres.2024.127863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 07/20/2024] [Accepted: 07/29/2024] [Indexed: 08/09/2024]
Abstract
High-throughput sequencing studies have shown that diet or antimicrobial treatments impact animal gut microbiota equilibrium. However, properties related to the gut microbial ecosystem stability, such as resilience, resistance, or functional redundancy, must be better understood. To shed light on these ecological processes, we combined advanced statistical methods with 16 S rRNA gene sequencing, functional prediction, and fitness analyses in the gut microbiota of the cockroach Blattella germanica subject to three periodic pulses of the antibiotic (AB) kanamycin (n=512). We first confirmed that AB did not significantly affect cockroaches' biological fitness, and gut microbiota changes were not caused by insect physiology alterations. The sex variable was examined for the first time in this species, and no statistical differences in the gut microbiota diversity or composition were found. The comparison of the gut microbiota dynamics in control and treated populations revealed that (1) AB treatment decreases diversity and completely disrupts the co-occurrence networks between bacteria, significantly altering the gut community structure. (2) Although AB also affected the genetic composition, functional redundancy would explain a smaller effect on the functional potential than on the taxonomic composition. (3) As predicted by Taylor's law, AB generally affected the most abundant taxa to a lesser extent than the less abundant taxa. (4) Taxa follow different trends in response to ABs, highlighting "resistant taxa," which could be critical for community restoration. (5) The gut microbiota recovered faster after the three AB pulses, suggesting that gut microbiota adapts to repeated treatments.
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Affiliation(s)
- Jesús Marín-Miret
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish Research Council, Paterna, Valencia 46980, Spain; Genomic and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research of the Valencia Region, Valencia 46020, Spain
| | - Ana Elena Pérez-Cobas
- Department of Microbiology, Ramón y Cajal Institute for Health Research (IRYCIS), Ramón y Cajal University Hospital, Madrid, Spain; CIBER in Infectious Diseases (CIBERINFEC), Madrid, Spain
| | - Rebeca Domínguez-Santos
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish Research Council, Paterna, Valencia 46980, Spain
| | - Benjamí Pérez-Rocher
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish Research Council, Paterna, Valencia 46980, Spain
| | - Amparo Latorre
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish Research Council, Paterna, Valencia 46980, Spain; Genomic and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research of the Valencia Region, Valencia 46020, Spain
| | - Andrés Moya
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and Spanish Research Council, Paterna, Valencia 46980, Spain; Genomic and Health Area, Foundation for the Promotion of Sanitary and Biomedical Research of the Valencia Region, Valencia 46020, Spain.
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3
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Wang K, Miao Y, Liu W, Muhammad I, Bao J, Jin X, Wu Z, Li R, Chen C, Li J. Lactobacillus salivarius ameliorates Mycoplasma gallisepticum-induced inflammation via the JAK/STAT signaling pathway involving respiratory microbiota and metabolites. Poult Sci 2024; 103:103942. [PMID: 38908119 PMCID: PMC11246048 DOI: 10.1016/j.psj.2024.103942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/20/2024] [Accepted: 05/30/2024] [Indexed: 06/24/2024] Open
Abstract
Mycoplasma gallisepticum (MG) can cause chronic respiratory disease (CRD) in chickens, which has a significant negative economic impact on the global poultry sector. Respiratory flora is the guardian of respiratory health, and its disorder is closely related to respiratory immunity and respiratory diseases. As a common probiotic in the chicken respiratory tract, Lactobacillus salivarius (L. salivarius) has potential antioxidant, growth performance enhancing, and anti-immunosuppressive properties. However, the specific mechanism through which L. salivarius protects against MG infection has not yet been thoroughly examined. This study intends to investigate whether L. salivarius could reduce MG-induced tracheal inflammation by modulating the respiratory microbiota and metabolites. The results indicated that L. salivarius reduced MG colonization significantly and alleviated the anomalous morphological changes by using the MG-infection model. L. salivarius also reduced the level of Th1 cell cytokines, increased the level of Th2 cell cytokines, and ameliorated immune imbalance during MG infection. In addition, L. salivarius improved the mucosal barrier, heightened immune function, and suppressed the Janus kinase/Signal transducer, and activator of transcription (JAK/STAT) signaling pathway. Notably, MG infection changed the composition of the respiratory microbiota and metabolites, and L. salivarius therapy partially reversed the aberrant respiratory microbiota and metabolite composition. Our results highlighted that these findings demonstrated that L. salivarius played a role in MG-mediated inflammatory damage and demonstrated that L. salivarius, by altering the respiratory microbiota and metabolites, could successfully prevent MG-induced inflammatory injury in chicken trachea.
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Affiliation(s)
- Kexin Wang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Xiangfang District, Harbin 150030, P. R. China
| | - Yusong Miao
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Xiangfang District, Harbin 150030, P. R. China; Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, P. R. China
| | - Weiqi Liu
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Xiangfang District, Harbin 150030, P. R. China
| | - Ishfaq Muhammad
- College of Computer Science, Huanggang Normal University, Huanggang, 438000, P. R. China
| | - Jiaxin Bao
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Xiangfang District, Harbin 150030, P. R. China
| | - Xiaodi Jin
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Xiangfang District, Harbin 150030, P. R. China
| | - Zhiyong Wu
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Xiangfang District, Harbin 150030, P. R. China
| | - Rui Li
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Xiangfang District, Harbin 150030, P. R. China
| | - Chunli Chen
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Xiangfang District, Harbin 150030, P. R. China; Department I of Pharmacology, Center for Pharmacology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, 50931, Germany
| | - Jichang Li
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Xiangfang District, Harbin 150030, P. R. China.
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4
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Liu W, Li Y, Wu P, Guo X, Xu Y, Jin L, Zhao D. The intratumoral microbiota: a new horizon in cancer immunology. Front Cell Infect Microbiol 2024; 14:1409464. [PMID: 39135638 PMCID: PMC11317474 DOI: 10.3389/fcimb.2024.1409464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 07/01/2024] [Indexed: 08/15/2024] Open
Abstract
Over the past decade, advancements in high-throughput sequencing technologies have led to a qualitative leap in our understanding of the role of the microbiota in human diseases, particularly in oncology. Despite the low biomass of the intratumoral microbiota, it remains a crucial component of the tumor immune microenvironment, displaying significant heterogeneity across different tumor tissues and individual patients. Although immunotherapy has emerged a major strategy for treating tumors, patient responses to these treatments vary widely. Increasing evidence suggests that interactions between the intratumoral microbiota and the immune system can modulate host tumor immune responses, thereby influencing the effectiveness of immunotherapy. Therefore, it is critical to gain a deep understanding of how the intratumoral microbiota shapes and regulates the tumor immune microenvironment. Here, we summarize the latest advancements on the role of the intratumoral microbiota in cancer immunity, exploring the potential mechanisms through which immune functions are influenced by intratumoral microbiota within and outside the gut barrier. We also discuss the impact of the intratumoral microbiota on the response to cancer immunotherapy and its clinical applications, highlighting future research directions and challenges in this field. We anticipate that the valuable insights into the interactions between cancer immunity and the intratumoral microbiota provided in this review will foster the development of microbiota-based tumor therapies.
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Affiliation(s)
- Wei Liu
- College of Laboratory Medicine, Jilin Medical University, Jilin, China
| | - Yuming Li
- College of Laboratory Medicine, Jilin Medical University, Jilin, China
| | - Ping Wu
- General Surgery Department of Liaoyuan Central Hospital, Jilin, China
| | - Xinyue Guo
- College of Laboratory Medicine, Jilin Medical University, Jilin, China
| | - Yifei Xu
- College of Laboratory Medicine, Jilin Medical University, Jilin, China
| | - Lianhai Jin
- Low Pressure and Low Oxygen Environment and Health Intervention Innovation Center, Jilin Medical University, Jilin, China
| | - Donghai Zhao
- College of Basic Medicine, Jilin Medical University, Jilin, China
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5
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Baquero F, Pérez-Cobas AE, Aracil-Gisbert S, Coque TM, Zamora J. Selection versus transmission: Quantitative and organismic biology in antibiotic resistance. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 121:105606. [PMID: 38768878 DOI: 10.1016/j.meegid.2024.105606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/12/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
We aimed to determine the importance of selection (mostly dependent on the anthropogenic use of antimicrobials) and transmission (mostly dependent on hygiene and sanitation) as drivers of the spread of antibiotic-resistant bacterial populations. The first obstacle to estimating the relative weight of both independent variables is the lack of detailed quantitative data concerning the number of bacterial cells, potentially either pathogenic or harmless, and bacterial species exposed to antimicrobial action in the microbiotas of specific environments. The second obstacle is the difficulty of considering the relative importance of the transmission and selection exerting their combined effects on antibiotic resistance across eco-biological levels. As a consequence, advances are urgently required in quantitative biology and organismic biology of antimicrobial resistance. The absolute number of humans exposed to antibiotics and the absolute number of potentially pathogenic and commensal bacteria in their microbiomes should influence both the selection and transmission of resistant bacterial populations. The "whole Earth" microbiome, with astonishingly high numbers of bacterial cells and species, which are also exposed to anthropogenic antimicrobials in various biogeographical spaces, shapes the antibiotic resistance landscape. These biogeographical spaces influence various intensities of selection and transmission of potentially pathogenic bacteria. While waiting for more precise data, biostatistics analysis and mathematical or computational modeling can provide proxies to compare the influence of selection and transmission in resistant bacteria. In European countries with lower sanitation levels, antibiotic consumption plays a major role in increasing antibiotic resistance; however, this is not the case in countries with high sanitation levels. Although both independent variables are linked, their relative influence on the level of antibiotic resistance varies according to the particular location. Therefore, interventions directed to decrease antibiotic resistance should be designed "a la carte" for specific locations with particular ecological conditions, including sanitation facilities.
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Affiliation(s)
- F Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain; Center for Biomedical Research in Epidemiology and Public Health Network (CIBERESP-Group 33), Madrid, Spain.
| | - A E Pérez-Cobas
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain; Center for Biomedical Research in Infectious Diseases Network (CIBERINFEC), Madrid, Spain
| | - S Aracil-Gisbert
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain; Center for Biomedical Research in Infectious Diseases Network (CIBERINFEC), Madrid, Spain
| | - T M Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain; Center for Biomedical Research in Infectious Diseases Network (CIBERINFEC), Madrid, Spain
| | - J Zamora
- Clinical Biostatistics Unit, Ramón y Cajal University Hospital, and Ramón y Cajal Institute for Health Research (IRYCIS) Madrid, Spain; Center for Biomedical Research in Epidemiology and Public Health Network (CIBERESP-Group 42), Madrid, Spain; Institute of Metabolism and Systems Research, Biostatistics in Maternal and Perinatal Health, University of Birmingham, UK
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6
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Kayongo A, Ntayi ML, Olweny G, Kyalo E, Ndawula J, Ssengooba W, Kigozi E, Kalyesubula R, Munana R, Namaganda J, Caroline M, Sekibira R, Bagaya BS, Kateete DP, Joloba ML, Jjingo D, Sande OJ, Mayanja-Kizza H. Airway microbiome signature accurately discriminates Mycobacterium tuberculosis infection status. iScience 2024; 27:110142. [PMID: 38904070 PMCID: PMC11187240 DOI: 10.1016/j.isci.2024.110142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/05/2024] [Accepted: 05/27/2024] [Indexed: 06/22/2024] Open
Abstract
Mycobacterium tuberculosis remains one of the deadliest infectious agents globally. Amidst efforts to control TB, long treatment duration, drug toxicity, and resistance underscore the need for novel therapeutic strategies. Despite advances in understanding the interplay between microbiome and disease in humans, the specific role of the microbiome in predicting disease susceptibility and discriminating infection status in tuberculosis still needs to be fully investigated. We investigated the impact of M.tb infection and M.tb-specific IFNγ immune responses on airway microbiome diversity by performing TB GeneXpert and QuantiFERON-GOLD assays during the follow-up phase of a longitudinal HIV-Lung Microbiome cohort of individuals recruited from two large independent cohorts in rural Uganda. M.tb rather than IFNγ immune response mainly drove a significant reduction in airway microbiome diversity. A microbiome signature comprising Streptococcus, Neisseria, Fusobacterium, Prevotella, Schaalia, Actinomyces, Cutibacterium, Brevibacillus, Microbacterium, and Beijerinckiacea accurately discriminated active TB from Latent TB and M.tb-uninfected individuals.
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Affiliation(s)
- Alex Kayongo
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
- Lung Institute, Makerere University College of Health Sciences, Kampala 256, Uganda
| | - Moses Levi Ntayi
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
- Lung Institute, Makerere University College of Health Sciences, Kampala 256, Uganda
| | - Geoffrey Olweny
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Edward Kyalo
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
- Lung Institute, Makerere University College of Health Sciences, Kampala 256, Uganda
| | - Josephine Ndawula
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
- Lung Institute, Makerere University College of Health Sciences, Kampala 256, Uganda
| | - Willy Ssengooba
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
- Lung Institute, Makerere University College of Health Sciences, Kampala 256, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Robert Kalyesubula
- Department of Research, African Community Center for Social Sustainability (ACCESS), Nakaseke 256, Uganda
- Department of Medicine, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Richard Munana
- Department of Research, African Community Center for Social Sustainability (ACCESS), Nakaseke 256, Uganda
| | - Jesca Namaganda
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
- Lung Institute, Makerere University College of Health Sciences, Kampala 256, Uganda
| | - Musiime Caroline
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Rogers Sekibira
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Bernard Sentalo Bagaya
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - David Patrick Kateete
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Moses Lutaakome Joloba
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Daudi Jjingo
- College of Computing and Information Sciences, Computer Science, Makerere University, Kampala 256, Uganda
- African Center of Excellence in Bioinformatics and Data Science, Infectious Diseases Institute, Kampala 256, Uganda
| | - Obondo James Sande
- Department of Immunology and Molecular Biology, Makerere University, College of Health Sciences, Kampala 256, Uganda
| | - Harriet Mayanja-Kizza
- Department of Medicine, Makerere University, College of Health Sciences, Kampala 256, Uganda
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Everard ML, Priftis K, Koumbourlis AC, Shields MD. Time to re-set our thinking about airways disease: lessons from history, the resurgence of chronic bronchitis / PBB and modern concepts in microbiology. Front Pediatr 2024; 12:1391290. [PMID: 38910961 PMCID: PMC11190372 DOI: 10.3389/fped.2024.1391290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 05/06/2024] [Indexed: 06/25/2024] Open
Abstract
In contrast to significant declines in deaths due to lung cancer and cardiac disease in Westernised countries, the mortality due to 'chronic obstructive pulmonary disease' (COPD) has minimally changed in recent decades while 'the incidence of bronchiectasis' is on the rise. The current focus on producing guidelines for these two airway 'diseases' has hindered progress in both treatment and prevention. The elephant in the room is that neither COPD nor bronchiectasis is a disease but rather a consequence of progressive untreated airway inflammation. To make this case, it is important to review the evolution of our understanding of airway disease and how a pathological appearance (bronchiectasis) and an arbitrary physiological marker of impaired airways (COPD) came to be labelled as 'diseases'. Valuable insights into the natural history of airway disease can be obtained from the pre-antibiotic era. The dramatic impacts of antibiotics on the prevalence of significant airway disease, especially in childhood and early adult life, have largely been forgotten and will be revisited as will the misinterpretation of trials undertaken in those with chronic (bacterial) bronchitis. In the past decades, paediatricians have observed a progressive increase in what is termed 'persistent bacterial bronchitis' (PBB). This condition shares all the same characteristics as 'chronic bronchitis', which is prevalent in young children during the pre-antibiotic era. Additionally, the radiological appearance of bronchiectasis is once again becoming more common in children and, more recently, in adults. Adult physicians remain sceptical about the existence of PBB; however, in one study aimed at assessing the efficacy of antibiotics in adults with persistent symptoms, researchers discovered that the majority of patients exhibiting symptoms of PBB were already on long-term macrolides. In recent decades, there has been a growing recognition of the importance of the respiratory microbiome and an understanding of the ability of bacteria to persist in potentially hostile environments through strategies such as biofilms, intracellular communities, and persister bacteria. This is a challenging field that will likely require new approaches to diagnosis and treatment; however, it needs to be embraced if real progress is to be made.
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Affiliation(s)
- Mark L Everard
- Division of Paediatrics & Child Health, University of Western Australia, Perth, WA, Australia
| | - Kostas Priftis
- Allergology and Pulmonology Unit, 3rd Paediatric Department, National and Kapodistrian University of Athens, Athens, Greece
| | - Anastassios C Koumbourlis
- Division of Pulmonary & Sleep Medicine, George Washington University School of Medicine & Health Sciences, Washington, DC, United States
| | - Michael D Shields
- Experimental Medicine, Queen's University Belfast, Belfast, United Kingdom
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Salgado S, Hernández‐Herreros N, Prieto MA. Controlling the expression of heterologous genes in Bdellovibrio bacteriovorus using synthetic biology strategies. Microb Biotechnol 2024; 17:e14517. [PMID: 38934530 PMCID: PMC11209729 DOI: 10.1111/1751-7915.14517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Bdellovibrio bacteriovorus HD100 is an obligate predatory bacterium that preys upon Gram-negative bacteria. It has been proposed to be applied as a "living antibiotic" in several fields such as agriculture or even medicine, since it is able to prey upon bacterial pathogens. Its interesting lifestyle makes this bacterium very attractive as a microbial chassis for co-culture systems including two partners. A limitation to this goal is the scarcity of suitable synthetic biology tools for predator domestication. To fill this gap, we have firstly adapted the hierarchical assembly cloning technique Golden Standard (GS) to make it compatible with B. bacteriovorus HD100. The chromosomal integration of the Tn7 transposon's mobile element, in conjunction with the application of the GS technique, has allowed the systematic characterization of a repertoire of constitutive and inducible promoters, facilitating the control of the expression of heterologous genes in this bacterium. PJExD/EliR proved to be an exceptional promoter/regulator system in B. bacteriovorus HD100 when precise regulation is essential, while the synthetic promoter PBG37 showed a constitutive high expression. These genetic tools represent a step forward in the conversion of B. bacteriovorus into an amenable strain for microbial biotechnology approaches.
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Affiliation(s)
- Sergio Salgado
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC)MadridSpain
- Department of Microbial and Plant BiotechnologyPolymer Biotechnology Group, Margarita Salas Center for Biological Research (CIB‐CSIC)MadridSpain
| | - Natalia Hernández‐Herreros
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC)MadridSpain
- Department of Microbial and Plant BiotechnologyPolymer Biotechnology Group, Margarita Salas Center for Biological Research (CIB‐CSIC)MadridSpain
| | - M. Auxiliadora Prieto
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy‐Spanish National Research Council (SusPlast‐CSIC)MadridSpain
- Department of Microbial and Plant BiotechnologyPolymer Biotechnology Group, Margarita Salas Center for Biological Research (CIB‐CSIC)MadridSpain
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9
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Reuben RC, Torres C. Bacteriocins: potentials and prospects in health and agrifood systems. Arch Microbiol 2024; 206:233. [PMID: 38662051 PMCID: PMC11045635 DOI: 10.1007/s00203-024-03948-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024]
Abstract
Bacteriocins are highly diverse, abundant, and heterogeneous antimicrobial peptides that are ribosomally synthesized by bacteria and archaea. Since their discovery about a century ago, there has been a growing interest in bacteriocin research and applications. This is mainly due to their high antimicrobial properties, narrow or broad spectrum of activity, specificity, low cytotoxicity, and stability. Though initially used to improve food quality and safety, bacteriocins are now globally exploited for innovative applications in human, animal, and food systems as sustainable alternatives to antibiotics. Bacteriocins have the potential to beneficially modulate microbiota, providing viable microbiome-based solutions for the treatment, management, and non-invasive bio-diagnosis of infectious and non-infectious diseases. The use of bacteriocins holds great promise in the modulation of food microbiomes, antimicrobial food packaging, bio-sanitizers and antibiofilm, pre/post-harvest biocontrol, functional food, growth promotion, and sustainable aquaculture. This can undoubtedly improve food security, safety, and quality globally. This review highlights the current trends in bacteriocin research, especially the increasing research outputs and funding, which we believe may proportionate the soaring global interest in bacteriocins. The use of cutting-edge technologies, such as bioengineering, can further enhance the exploitation of bacteriocins for innovative applications in human, animal, and food systems.
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Affiliation(s)
- Rine Christopher Reuben
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain.
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006, Logroño, Spain
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10
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Drigot ZG, Clark SE. Insights into the role of the respiratory tract microbiome in defense against bacterial pneumonia. Curr Opin Microbiol 2024; 77:102428. [PMID: 38277901 PMCID: PMC10922932 DOI: 10.1016/j.mib.2024.102428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 01/28/2024]
Abstract
The respiratory tract microbiome (RTM) is a microbial ecosystem inhabiting different niches throughout the airway. A critical role for the RTM in dictating lung infection outcomes is underlined by recent efforts to identify community members benefiting respiratory tract health. Obligate anaerobes common in the oropharynx and lung such as Prevotella and Veillonella are associated with improved pneumonia outcomes and activate several immune defense pathways in the lower airway. Colonizers of the nasal cavity, including Corynebacterium and Dolosigranulum, directly impact the growth and virulence of lung pathogens, aligning with robust clinical correlations between their upper airway abundance and reduced respiratory tract infection risk. Here, we highlight recent work identifying respiratory tract bacteria that promote airway health and resilience against disease, with a focus on lung infections and the underlying mechanisms driving RTM-protective benefits.
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Affiliation(s)
- Zoe G Drigot
- University of Colorado School of Medicine, Department of Otolaryngology, Aurora, CO 80045, USA
| | - Sarah E Clark
- University of Colorado School of Medicine, Department of Otolaryngology, Aurora, CO 80045, USA.
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11
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Pérez-Cobas AE, Ginevra C, Rusniok C, Jarraud S, Buchrieser C. The respiratory tract microbiome, the pathogen load, and clinical interventions define severity of bacterial pneumonia. Cell Rep Med 2023; 4:101167. [PMID: 37633274 PMCID: PMC10518590 DOI: 10.1016/j.xcrm.2023.101167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 06/18/2023] [Accepted: 08/02/2023] [Indexed: 08/28/2023]
Abstract
Bacterial pneumonia is a considerable problem worldwide. Here, we follow the inter-kingdom respiratory tract microbiome (RTM) of a unique cohort of 38 hospitalized patients (n = 97 samples) with pneumonia caused by Legionella pneumophila. The RTM composition is characterized by diversity drops early in hospitalization and ecological species replacement. RTMs with the highest bacterial and fungal loads show low diversity and pathogen enrichment, suggesting high biomass as a biomarker for secondary and/or co-infections. The RTM structure is defined by a "commensal" cluster associated with a healthy RTM and a "pathogen" enriched one, suggesting that the cluster equilibrium drives the microbiome to recovery or dysbiosis. Legionella biomass correlates with disease severity and co-morbidities, while clinical interventions influence the RTM dynamics. Fungi, archaea, and protozoa seem to contribute to progress of pneumonia. Thus, the interplay of the RTM equilibrium, the pathogen load dynamics, and clinical interventions play a critical role in patient recovery.
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Affiliation(s)
- Ana Elena Pérez-Cobas
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, Paris, France; CNRS UMR 6047, 75724 Paris, France.
| | - Christophe Ginevra
- Hospices Civils de Lyon, Centre National de Référence des Légionelles, Bron, France; Centre International de Recherche en Infectiologie, Université Lyon 1, UMR CNRS 5308, U1111 Inserm, École Normale Supérieure de Lyon, Lyon, France
| | - Christophe Rusniok
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, Paris, France; CNRS UMR 6047, 75724 Paris, France
| | - Sophie Jarraud
- Hospices Civils de Lyon, Centre National de Référence des Légionelles, Bron, France; Centre International de Recherche en Infectiologie, Université Lyon 1, UMR CNRS 5308, U1111 Inserm, École Normale Supérieure de Lyon, Lyon, France
| | - Carmen Buchrieser
- Institut Pasteur, Université Paris Cité, Biologie des Bactéries Intracellulaires, Paris, France; CNRS UMR 6047, 75724 Paris, France.
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Hernandez-Leyva AJ, Rosen AL, Tomera CP, Lin EE, Akaho EH, Blatz AM, Otto WR, Logan J, Young LR, Harris RM, Kau AL, John ARO. Developmental progression of the nasopharyngeal microbiome during childhood and association with the lower airway microbiome. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.18.23295747. [PMID: 37790477 PMCID: PMC10543049 DOI: 10.1101/2023.09.18.23295747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Background The upper (URT) and lower (LRT) respiratory tract feature distinct environments and responses affecting microbial colonization but investigating the relationship between them is technically challenging. We aimed to identify relationships between taxa colonizing the URT and LRT and explore their relationship with development during childhood. Methods We employed V4 16S rDNA sequencing to profile nasopharyngeal swabs and tracheal aspirates collected from 183 subjects between 20 weeks and 18 years of age. These samples were collected prior to elective procedures at the Children's Hospital of Philadelphia over the course of 20 weeks in 2020, from otherwise healthy subjects enrolled in a study investigating potential reservoirs of SARS-CoV-2. Findings After extraction, sequencing, and quality control, we studied the remaining 124 nasopharyngeal swabs and 98 tracheal aspirates, including 85 subject-matched pairs of samples. V4 16S rDNA sequencing revealed that the nasopharynx is colonized by few, highly-abundant taxa, while the tracheal aspirates feature a diverse assembly of microbes. While no taxa co-occur in the URT and LRT of the same subject, clusters of microbiomes in the URT correlate with clusters of microbiomes in the LRT. The clusters identified in the URT correlate with subject age across childhood development. Interpretations The correlation between clusters of taxa across sites may suggest a mutual influence from either a third site, such as the oropharynx, or host-extrinsic, environmental features. The identification of a pattern of upper respiratory microbiota development across the first 18 years of life suggests that the patterns observed in early childhood may extend beyond the early life window.
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Affiliation(s)
- Ariel J Hernandez-Leyva
- Division of Allergy and Immunology, Department of Medicine and Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Anne L Rosen
- Division of Allergy and Immunology, Department of Medicine and Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Christopher P Tomera
- Division of Allergy and Immunology, Department of Medicine and Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Elaina E Lin
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Anesthesiology and Critical Care Medicine, Children's Hospital of Philadelphia, Philadelphia PA
| | - Elikplim H Akaho
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia PA
- Department of Medicine, John H. Stroger, Jr. Hospital of Cook County
| | - Allison M Blatz
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia PA
- Division of Critical Care Medicine, Department of Pediatrics, Nemours Children's Hospital, Wilmington DE
| | - William R Otto
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia PA
- Division of Infectious Disease, Cincinnati Children's Hospital Medical Center; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Joey Logan
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia PA
| | - Lisa R Young
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia PA
| | - Rebecca M Harris
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia PA
| | - Andrew L Kau
- Division of Allergy and Immunology, Department of Medicine and Center for Women's Infectious Disease Research, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Audrey R Odom John
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Infectious Diseases, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia PA
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